Identification of long noncoding RNAs in Schistosoma mansoni and Schistosoma japonicum

• Published in: Experimental parasitology 2018-08, Vol.191, p.82-87
• Main Authors: Liao, Qi, Zhang, Yuwei, Zhu, Yuchao, Chen, Jia, Dong, Changzheng, Tao, Yang, He, Ai, Liu, Jianfa, Wu, Zhongdao
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Conserved Sequence; Female; Histones - metabolism; Long noncoding RNAs (lncRNAs); Male; Promoter Regions, Genetic; RNA, Helminth - chemistry; RNA, Long Noncoding - isolation & purification; RNA-seq; Schistosoma haematobium - genetics; Schistosoma japonicum; Schistosoma japonicum - genetics; Schistosoma mansoni; Schistosoma mansoni - genetics; Schistosomiasis - diagnosis; Schistosomiasis - parasitology; Schistosomiasis - prevention & control; Sequence Alignment; Transcriptome - genetics
• ISSN: 0014-4894; 1090-2449
• DOI: 10.1016/j.exppara.2018.07.001

Schistosomiasis is a major parasitic disease caused by 3 principal species of schistosome. Studies of schistosome transcriptomes have focused on protein-coding transcripts and although miRNAs are attracting increased attention, few reports have concerned the long noncoding RNAs (lncRNAs). These have been shown to play key roles in the regulation of gene expression through interactions with mRNAs, proteins and miRNAs. In this study, we first identified lncRNAs from RNA-seq data in Schistosoma mansoni and Schistosoma japonicum: 3247 and 3033 potential lncRNAs were found in these two species respectively. ChIP-seq analysis to determine H3K4me3 profiles along the gene regions corresponding to lncRNAs showed that in 12% of cases this mark was enriched in regions proximal to the transcription start sites, supporting their validity as actively transcribed genes. Besides, the sequence conservation of lncRNAs between schistosome species was much lower than that of mRNAs, but higher than that of the randomly selected genomic sequences, which is consistent with that in mammals. Our results demonstrate that lncRNAs form a significant part of the schistosome transcriptome and suggest that they play an important role in the biology of the parasite. [Display omitted] •A total of 3247 and 3033 lncRNAs were identified in Schistosoma mansoni and Schistosoma japonicum.•More H3K4me3 marked promoters of lncRNAs were detected compared with randomly selected sequences from noncoding regions.•LncRNAs are less conserved than mRNAs but more than the randomly selected sequences, which supports their functionality.